This chapter discusses about taxonomy and classification of viruses. For viruses, the process of comparative analysis plays a critical role in increasing our overall knowledge of the molecular biology, pathogenesis, epidemiology, and evolution of poorly understood or newly isolated viruses. This knowledge enhances our ability to respond to new threats by supporting the development of diagnostics, vaccines, and other antiviral therapies. In fact, it is likely that viruses have multiple independent evolutionary origins that cannot be easily or completely separated from the evolution of their hosts, as they cannot reproduce or evolve separately from their hosts. Therefore, viruses might be better represented as individual twigs arising from branches spread throughout the rest of the tree. In addition to distinct evolutionary histories, viruses differ from other domains of life in the variety of possible coding molecules they utilize to store their genetic programs. For viruses, the Virology Division of the International Union of Microbiological Societies has charged the International Committee on Taxonomy of Viruses (ICTV) with the task of developing, refining, and maintaining a universal viral taxonomy. As categorized according to the 2009 ICTV taxonomy, viruses that infect humans fall into 4 orders: the Herpesvirales, Mononegavirales, Nidovirales, and Picornavirales. The ICTV produces an extensive amount of information during the process of classifying and naming viruses that is published regularly in the ICTV reports.

Taxonomic demarcation via sequence similarity. (A) PASC was carried out on the viral DNA-dependent DNA polymerase gene (the vaccinia virus E9L gene homolog) for every completely sequenced poxvirus genome. Each protein was aligned to every other protein, and the percent identity of each pairwise comparison was then included in a histogram plot of all possible comparisons. Peaks are identified across the top of the figure according to the taxa represented by particular pairwise sequence comparisons. (B) Phylogenetic reconstruction of the Poxviridae family of viruses based on their DNA polymerase protein sequences. Subfamily and genera demarcations are identified. Terminal nodes are labeled according to genus. Sequences belonging to one of the genera labeled either group A or B coincide with the A and B comparison peaks at the top of panel A. (C) Phylogenetic prediction based on the multiple nucleic acid sequence alignment of the core genomic region of each representative orthopoxvirus species or strain. BR, strain Brighton Red; GRI, strain GRI-90. Reprinted with modification from Virus Research (30) with permission of the publisher.

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10.1128/9781555816728/fig75-1.gif

FIGURE 1

Taxonomic demarcation via sequence similarity. (A) PASC was carried out on the viral DNA-dependent DNA polymerase gene (the vaccinia virus E9L gene homolog) for every completely sequenced poxvirus genome. Each protein was aligned to every other protein, and the percent identity of each pairwise comparison was then included in a histogram plot of all possible comparisons. Peaks are identified across the top of the figure according to the taxa represented by particular pairwise sequence comparisons. (B) Phylogenetic reconstruction of the Poxviridae family of viruses based on their DNA polymerase protein sequences. Subfamily and genera demarcations are identified. Terminal nodes are labeled according to genus. Sequences belonging to one of the genera labeled either group A or B coincide with the A and B comparison peaks at the top of panel A. (C) Phylogenetic prediction based on the multiple nucleic acid sequence alignment of the core genomic region of each representative orthopoxvirus species or strain. BR, strain Brighton Red; GRI, strain GRI-90. Reprinted with modification from Virus Research (30) with permission of the publisher.

Virion morphology. Depiction of the shapes and sizes of viruses of families that include animal, zoonotic, and human pathogens. The virions are drawn to scale, but artistic license has been used in representing their structure. In some, the cross-sectional structure of capsid and envelope are shown, with a representation of the genome; with the very small virions, only their size and symmetry are depicted. RT, reverse transcribing; +, positive-sense genome; -, negativesense genome. Reprinted with modification from Virus Taxonomy. Eighth Report of the International Committee on Taxonomy of Viruses (16) with permission of the publisher.

10.1128/9781555816728/fig75-2_thmb.gif

10.1128/9781555816728/fig75-2.gif

FIGURE 2

Virion morphology. Depiction of the shapes and sizes of viruses of families that include animal, zoonotic, and human pathogens. The virions are drawn to scale, but artistic license has been used in representing their structure. In some, the cross-sectional structure of capsid and envelope are shown, with a representation of the genome; with the very small virions, only their size and symmetry are depicted. RT, reverse transcribing; +, positive-sense genome; -, negativesense genome. Reprinted with modification from Virus Taxonomy. Eighth Report of the International Committee on Taxonomy of Viruses (16) with permission of the publisher.

22.International Committee on Nomenclature of Viruses, and P.Wildy. 1971. Classification and Nomenclature of Viruses. First Report of the International Committee on Nomenclature of Viruses.S. Karger, Basel, Switzerland.